Figure 1. Comparative metagenomic analysis of plasmids resident in the human gut microbiome (After Jones et al. 2010, BMC Genomics 11:46)
A) The complete nucleotide sequence of plasmids was used to search 15 human gut metagenomes, the combined gut metagenome of lean and obese mice, Sargasso Sea, and soil metagenomes. The central ring shows the physical plasmid map with encoded ORFs. Concentric rings represent the nine human gut metagenomes in which homologous sequences were identified, and bars indicate regions of homology between sequences retrieved from human gut metagenomes and corresponding regions of the pTRACA10 or pTRACA22 plasmids. Colours of bars indicate the % identity at the nucleotide level for each metagenomic sequence: ■ = 80 to 85% identity, ■ = 85 to 90% identity, ■ = 90 to 96% identity. Only sequences >100bp in length are shown. B) Relative abundance of pTRACA22 ORFs, expressed as hits/Mb, in the combined human gut metagenomes of 15 individuals compared to the combined murine gut metagenome, Sargasso Sea, and soil metagenomes. The observed differences between human and non-human metagenomes were explored using the χ2 distribution. Symbols above bars indicate approximate significance of differences between combined human metagenomes and each non-human metagenomes (P = 0.01 or less): ● Significant difference between human and murine metagenomes; ● Significant difference between human and marine metagenomes; ● Significant difference between human and soil metagenomes. ORF22-6 and ORF22-7 comprise the pTRACA22 RelBE toxin anti-toxin (TA) module and are among the most enriched functions encoded by this plasmid. C) Relative abundance (as hits/Mb) of the pTRACA22 RelBE TA module (ORF22-6 and ORF22-7 in part A and B) in human gut, murine gut and environmental metagenomes, compared to relative abundance of MazEF, ParDE and HigBA TA modules. The observed differences between human and non-human metagenomes were explored using the χ2 distribution. Symbols above bars indicate approximate significance of differences between combined human metagenomes and each non-human metagenome (P = 0.01 or less), as in Figure 1B.
true components of the human ‘superorganism’ with the genetic content of our microbial partners often referred to as the second human genome (5, 6, 9, 20). Many researchers now consider complex metazoans such as mammals to be amalgams of both eukaryotic cells and their prokaryotic symbionts, rather than being exclusively eukaryotic (5, 6,
9, 20, 21). This has given rise to new ecological and evolutionary theories, which integrate host-associated communities into the development of the higher organisms they colonize (5, 6, 9, 21, 22). In this context, the mobile metagenome may constitute a key resource in the adaptation of both host and microbe, by providing access to an
immense genetic resource through which community function, and fitness of both host and microbe may be augmented (9). Although the study of the mobile metagenome, and the theories surrounding this concept are of significant interest and importance from a fundamental standpoint alone, there is 47